Contribute to TopFIND

You have to sign up and log in to be able to contribute data.

Intdroduction

Your data submission is highly valuable to us. We have assembled a short picture guide on how to enter your experimental information and batch upload your protein termini, cleavages, cleavage sites or inhibition. Please contact us if there are any questions or you want to enquire about other options for batch data import (e.g. when you already have your data in a structured form, or for example in a database). Even though the 3 step process below is very straight forward we are always happy to find even more efficient ways.

Step 1: Login/Signup

Please login:


or signup:


Step 2: Create Evidence

Please create an evidence entry describing the source of the contributed information


Step 3: Import excel file

Please upload a comma seperated (csv) or excel file including a header line. You can contribute five kinds of data:

  1. proteases cleaving a native protein
    please provide the data in the following order using the headerline: protease,position,substrate
    • protease: UniProt ID: Q9BYF1
    • position: cleavage site position in the form: 222-223
    • substrate: UniProt ID: Q9BYF1
  2. proteases cleaving a peptide
    please provide the data in the following order using the headerline: protease,peptide
    • protease: UniProt ID: Q9BYF1
    • peptide: peptide sequence with the cleavage site indicated by a colon: GA:GQCVFA
  3. proteases inhibited by protein inhibitors
    please provide the data in the following order using the headerline: protease,inhibitor
    • protease: UniProt ID: Q9BYF1
    • peptide: UniProt ID: Q9BYF1
  4. protein N-termini
    please provide the data in the following order using the headerline: protein,position,modification,confidence,confidence_type
    • protein: UniProt ID: Q9BYF1
    • position: first amino acid relative to UniProt full length protein sequence: 222
    • modification: name of the modification of the first amino acid according to TopFIND (link: modifications - use the filter on the right to find a modification): acteylation or N-acetylaspartate
    • confidence: a confidence measurement if applicable (e.g. when based on peptide identification by mass spectrometry)
    • confidence type: The type of the confidence value given (any of: 'unknown','probability','MASCOT score','X! Tandem score','PeptideProphet probability')
  5. protein C-termini
    please provide the data in the following order using the headerline: protein,position,modification,confidence,confidence_type
    • protein: UniProt ID: Q9BYF1
    • position: last amino acid relative to UniProt full length protein sequence: 221
    • modification: name of the modification of the last amino acid according to TopFIND (link: modifications - use the filter on the right to find a modification): acteylation or N-acetylaspartate
    • confidence: a confidence measurement if applicable (e.g. when based on peptide identification by mass spectrometry)
    • confidence type: The type of the confidence value given (any of: 'unknown','probability','MASCOT score','X! Tandem score','PeptideProphet probability')


Please contact 'philipp.lange@ubc.ca' in case of problems or further questions.